From eb88a15ad2afd22a72fddf632d45511c33f23488 Mon Sep 17 00:00:00 2001
From: Leonid Kostrykin <void@evoid.de>
Date: Wed, 15 Nov 2023 21:33:34 +0100
Subject: [PATCH] refactors recent superdsm changes using select param

---
 tools/superdsm/superdsm.xml | 168 +++++++++++++++---------------------
 1 file changed, 69 insertions(+), 99 deletions(-)

diff --git a/tools/superdsm/superdsm.xml b/tools/superdsm/superdsm.xml
index cf778245..221786ec 100644
--- a/tools/superdsm/superdsm.xml
+++ b/tools/superdsm/superdsm.xml
@@ -20,70 +20,65 @@
     </requirements>
     <command detect_errors="aggressive">
     <![CDATA[
-    #if $do_masks_enabled == 'true' or $do_cfg_enabled == 'true' or $do_overlay.do_overlay_enabled == 'true':
-        python '$__tool_directory__/run-superdsm.py'
-        '${dataset}'
-        \${GALAXY_SLOTS:-4}
-        #if $do_masks_enabled == 'true':
-            --do-masks 'masks.png'
-        #end if
-        #if $do_cfg_enabled == 'true':
-            --do-cfg 'cfg.tsv'
-        #end if
-        #if $do_overlay.do_overlay_enabled == 'true':
-            --do-overlay 'overlay.png'
-            #if $seg_border.value % 2 == 1:
-                #set $seg_border = "%d" % ($seg_border.value + 1)
-                --do-overlay-border $seg_border
-            #else:
-                --do-overlay-border $seg_border
-            #end if
-        #end if
-        #if str($config.AF_scale) != '':
-            --AF_scale '${config.AF_scale}'
-        #end if
-        #if str($config.c2f_region_analysis_min_atom_radius) != '':
-            --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
-        #end if
-        #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
-            --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
-        #end if
-        #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
-            --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
-        #end if
-        #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
-            --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
-        #end if
-        #if str($config.dsm_alpha) != '':
-            --dsm_alpha '${config.dsm_alpha}'
-        #end if
-        #if str($config.dsm_AF_alpha) != '':
-            --dsm_AF_alpha '${config.dsm_AF_alpha}'
-        #end if
-        #if str($config.global_energy_minimization_beta) != '':
-            --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
-        #end if
-        #if str($config.global_energy_minimization_AF_beta) != '':
-            --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
-        #end if
-        #if str($config.postprocess_mask_max_distance) != '':
-            --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
-        #end if
-        #if str($config.postprocess_mask_stdamp) != '':
-            --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
-        #end if
-        #if str($config.postprocess_max_norm_energy) != '':
-            --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
-        #end if
-        #if str($config.postprocess_min_contrast) != '':
-            --postprocess_min_contrast '${config.postprocess_min_contrast}'
-        #end if
-        #if str($config.postprocess_min_object_radius) != '':
-            --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
+    python '$__tool_directory__/run-superdsm.py'
+    '${dataset}'
+    \${GALAXY_SLOTS:-4}
+    #if 'masks' in $outputs:
+        --do-masks 'masks.png'
+    #end if
+    #if 'cfg' in $outputs:
+        --do-cfg 'cfg.tsv'
+    #end if
+    #if 'overlay' in $outputs:
+        --do-overlay 'overlay.png'
+        #if $seg_border.value % 2 == 1:
+            #set $seg_border = "%d" % ($seg_border.value + 1)
+            --do-overlay-border $seg_border
+        #else:
+            --do-overlay-border $seg_border
         #end if
-    #else
-        echo "No outputs selected."
-        exit 1
+    #end if
+    #if str($config.AF_scale) != '':
+        --AF_scale '${config.AF_scale}'
+    #end if
+    #if str($config.c2f_region_analysis_min_atom_radius) != '':
+        --c2f_region_analysis_min_atom_radius '${config.c2f_region_analysis_min_atom_radius}'
+    #end if
+    #if str($config.c2f_region_analysis_min_norm_energy_improvement) != '':
+        --c2f_region_analysis_min_norm_energy_improvement '${config.c2f_region_analysis_min_norm_energy_improvement}'
+    #end if
+    #if str($config.c2f_region_analysis_max_atom_norm_energy) != '':
+        --c2f_region_analysis_max_atom_norm_energy '${config.c2f_region_analysis_max_atom_norm_energy}'
+    #end if
+    #if str($config.c2f_region_analysis_max_cluster_marker_irregularity) != '':
+        --c2f_region_analysis_max_cluster_marker_irregularity '${config.c2f_region_analysis_max_cluster_marker_irregularity}'
+    #end if
+    #if str($config.dsm_alpha) != '':
+        --dsm_alpha '${config.dsm_alpha}'
+    #end if
+    #if str($config.dsm_AF_alpha) != '':
+        --dsm_AF_alpha '${config.dsm_AF_alpha}'
+    #end if
+    #if str($config.global_energy_minimization_beta) != '':
+        --global_energy_minimization_beta '${config.global_energy_minimization_beta}'
+    #end if
+    #if str($config.global_energy_minimization_AF_beta) != '':
+        --global_energy_minimization_AF_beta '${config.global_energy_minimization_AF_beta}'
+    #end if
+    #if str($config.postprocess_mask_max_distance) != '':
+        --postprocess_mask_max_distance '${config.postprocess_mask_max_distance}'
+    #end if
+    #if str($config.postprocess_mask_stdamp) != '':
+        --postprocess_mask_stdamp '${config.postprocess_mask_stdamp}'
+    #end if
+    #if str($config.postprocess_max_norm_energy) != '':
+        --postprocess_max_norm_energy '${config.postprocess_max_norm_energy}'
+    #end if
+    #if str($config.postprocess_min_contrast) != '':
+        --postprocess_min_contrast '${config.postprocess_min_contrast}'
+    #end if
+    #if str($config.postprocess_min_object_radius) != '':
+        --postprocess_min_object_radius '${config.postprocess_min_object_radius}'
     #end if
     ]]>
     </command>
@@ -92,27 +87,12 @@
     </environment_variables>
     <inputs>
         <param name="dataset" type="data" format="tiff,png" label="Dataset" />
-        <section name="outputs" title="Outputs" expanded="true">
-            <conditional name="do_overlay">
-                <param name="do_overlay_enabled" type="select" label="Segmentation overlay">
-                    <option value="true" selected="true">Create a segmentation overlay</option>
-                    <option value="false">Do not create a segmentation overlay</option>
-                </param>
-                <when value="true">
-                    <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" />
-                </when>
-                <when value="false">
-                </when>
-            </conditional>
-            <param name="do_masks_enabled" type="select" label="Label map">
-                <option value="true">Create a label map (e.g., for further processing)</option>
-                <option value="false" selected="true">Do not create a label map</option>
-            </param>
-            <param name="do_cfg_enabled" type="select" label="Hyperparameters">
-                <option value="true">Report all hyperparameters (manually set and automatically determined values)</option>
-                <option value="false" selected="true">Do not report the values of the hyperparamters</option>
-            </param>
-        </section>
+        <param name="outputs" type="select" label="Outputs" multiple="true" optional="false">
+            <option value="overlay" selected="true">Create a segmentation overlay</option>
+            <option value="masks">Create a label map (e.g., for further processing)</option>
+            <option value="cfg">Report all hyperparameters (manually set and automatically determined values)</option>
+        </param>
+        <param name="seg_border" type="integer" min="1" value="8" label="Width of the outlines (in pixels)" help="This parameter is only used for segmentation overlays (see above)." />
         <section name="config" title="Hyperparameters" expanded="false">
             <param argument="--AF_scale" optional="true" type="float" value="" min="0" label="scale σ" help="The scale of the objects to be segmented. Leave empty to use the automatically determined value." />
             <param argument="--c2f_region_analysis_min_atom_radius" optional="true" type="float" value="" min="0" label="min_atom_radius" help="No region determined by the Coarse-to-fine region analysis scheme is smaller than a circle of this radius (in terms of the surface area). Leave empty to use the automatically determined value." />
@@ -132,37 +112,27 @@
     </inputs>
     <outputs>
         <data format="png" name="masks" from_work_dir="masks.png" label="${tool.name} on ${on_string}: masks">
-            <filter>outputs['do_masks_enabled'] == 'true'</filter>
+            <filter>'masks' in outputs</filter>
         </data>
         <data format="tsv" name="cfg" from_work_dir="cfg.tsv" label="${tool.name} on ${on_string}: cfg">
-            <filter>outputs['do_cfg_enabled'] == 'true'</filter>
+            <filter>'cfg' in outputs</filter>
         </data>
         <data format="png" name="overlay" from_work_dir="overlay.png" label="${tool.name} on ${on_string}: overlay">
-            <filter>outputs['do_overlay']['do_overlay_enabled'] == 'true'</filter>
+            <filter>'overlay' in outputs</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="3">
             <param name="dataset" value="BBBC033_C2_z28.png" />
-            <param name="do_masks_enabled" value="true" />
-            <param name="do_overlay_enabled" value="true" />
-            <param name="do_cfg_enabled" value="true" />
+            <param name="outputs" value="overlay,masks,cfg" />
             <output name="overlay" value="overlay.png" ftype="png" compare="sim_size" />
             <output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
         </test>
         <test expect_num_outputs="1">
             <param name="dataset" value="BBBC033_C2_z28.png" />
-            <param name="do_masks_enabled" value="false" />
-            <param name="do_overlay_enabled" value="false" />
-            <param name="do_cfg_enabled" value="true" />
+            <param name="outputs" value="cfg" />
             <output name="cfg" value="cfg.tsv" ftype="tsv" compare="sim_size" />
         </test>
-        <test expect_failure="true">
-            <param name="dataset" value="BBBC033_C2_z28.png" />
-            <param name="do_masks_enabled" value="false" />
-            <param name="do_overlay_enabled" value="false" />
-            <param name="do_cfg_enabled" value="false" />
-        </test>
     </tests>
     <help>
         This tool permits the segmentation of cell nuclei in 2-D fluorescence microscopy images.